Merge branch 'devel' into master

.github/workflows/rworkflows.yml

@@ -0,0 +1,57 @@
+name: rworkflows
+'on':
+  push:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+  pull_request:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+jobs:
+  rworkflows:
+    permissions: write-all
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: ghcr.io/bioconductor/bioconductor_docker:devel
+          rspm: ~
+        - os: macOS-latest
+          bioc: devel
+          r: auto
+          cont: ~
+          rspm: ~
+        - os: windows-latest
+          bioc: devel
+          r: auto
+          cont: ~
+          rspm: ~
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ false }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ true }}
+        run_pkgdown: ${{ true }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1
+        docker_registry: ghcr.io

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: miaViz
 Title: Microbiome Analysis Plotting and Visualization
-Version: 1.11.0
+Version: 1.13.1
 Authors@R: 
     c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
              email = "[email protected]",
@@ -61,6 +61,8 @@ Suggests:
     vegan,
     microbiomeDataSets,
     bluster
+Remotes:
+    github::microbiome/miaTime
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 VignetteBuilder: knitr

NAMESPACE

@@ -5,6 +5,7 @@ export(plotCCA)
 export(plotColGraph)
 export(plotColTile)
 export(plotDMNFit)
+export(plotFeaturePrevalence)
 export(plotPrevalence)
 export(plotPrevalentAbundance)
 export(plotRDA)
@@ -23,6 +24,7 @@ exportMethods(plotColGraph)
 exportMethods(plotColTile)
 exportMethods(plotColTree)
 exportMethods(plotDMNFit)
+exportMethods(plotFeaturePrevalence)
 exportMethods(plotPrevalence)
 exportMethods(plotPrevalentAbundance)
 exportMethods(plotRDA)
@@ -55,6 +57,7 @@ importFrom(SummarizedExperiment,assay)
 importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,rowData)
 importFrom(ape,as.phylo)
+importFrom(ape,drop.tip)
 importFrom(ape,keep.tip)
 importFrom(ape,rotateConstr)
 importFrom(dplyr,"%>%")
@@ -74,7 +77,7 @@ importFrom(dplyr,ungroup)
 importFrom(ggnewscale,new_scale)
 importFrom(ggnewscale,new_scale_colour)
 importFrom(ggnewscale,new_scale_fill)
-importFrom(ggplot2,aes_string)
+importFrom(ggplot2,aes)
 importFrom(ggplot2,coord_flip)
 importFrom(ggplot2,element_blank)
 importFrom(ggplot2,element_text)

NEWS

@@ -23,3 +23,7 @@ Changes in version 1.9.x
 + Added plotCCA and plotRDA functions
 
 Changes in version 1.11.x
++ replace addTaxonomyTree with addHierarchyTree after renaming in mia package
+
+Changes in version 1.13.x
++ plot*Tree: bugfix, ununique nodes